Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] \                     done.
Writing output ct file...done.
Single strand folding complete.
Initializing nucleic acids...done.
Applying SHAPE constraints...done.
Calculating free energies...done.
efn2 complete.
Converting CT file...CT file conversion complete.
/disk1/www/rails/humanrnamap/cli/./main.py:567: DeprecationWarning: Call to deprecated function (or staticmethod) VARNA. (Class has been renamed 'Structure')
  v = VARNA(structure=fold_dbn, sequence=seq)
Output file: /disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/final_image/SON_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.89 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.89 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.89 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.54 MB
Based on canonical annotations, the following gene is in your area of interest: SON(+)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 172.54 MB
Length of region: 91 nt.
100.0% of the region's A/C bases included in the filtered DMS dataset. Ideally, this number should be as high as possible for an experimenally-accurate prediction, and over 70% is recommended.
write dat - Elapsed time since the previous call: 0.17 seconds
write dat - Current memory usage: 176.05 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.05 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.45 seconds
efn2 - Current memory usage: 176.05 MB
This region has 1 predicted structures. 5 is the maximum structures visible on the web server. For up to 20 predictions per region, download and run the code locally.
Running command: /disk1/www/rails/humanrnamap/cli/bin/ct2dot "/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.05 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUCAAGUAAUACCAACUGAGGUGGCUAUAGAGUCCACACCAAUGAUACUGGAAUCUAGUAUCAUGUCAUCACAUGUUAUGAAAGGAAUUAA', '-structureDBN', '((((.((.......))))))((((((....)).))))....((((((((((...)))))))))).((((........))))..........', '-o', '/disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/final_image/SON_fold_1.svg', '-title', 'SON, -28.9 ± 0.7\n kcal/mol, AUC: 0.915', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,6,7,10,17,18,20,21,22,23,24,26,28,30,32,33,43,44,46,49,50,51,54,56,58,59,61,64,65,66,69,74,75,76,77,79,80,84,85,88,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,34,35,36,45,47,48,25,60,63,62,57', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '3,67,37,9,41,42,14,55', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '4,5,68,70,8,71,72,11,12,13,73,15,16,78,81,19,82,83,86,87,90,27,91,29,31,38,39,40,52,53']
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Text: 'G', X: 41.06561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 41.06561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 41.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 58.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 58.56561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 58.56561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 58.56561886658267, Y: 158.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 54.75001562590472, Y: 141.8727242422707, Width: 10.5, Height: 8
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Text: 'U', X: 46.23852378033553, Y: 123.77425727507122, Width: 10.5, Height: 8
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Text: 'A', X: 35.734355723682455, Y: 109.77733957744309, Width: 10.5, Height: 8
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Text: 'U', X: 39.957044909048136, Y: 92.79440262176948, Width: 10.5, Height: 8
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Text: 'A', X: 55.79323586528528, Y: 85.34683203840609, Width: 10.5, Height: 8
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Text: 'G', X: 71.5670297536627, Y: 92.9256629484855, Width: 10.5, Height: 8
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Text: 'A', X: 75.64853260203463, Y: 109.9430830260213, Width: 10.5, Height: 8
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Text: 'G', X: 84.1600244476038, Y: 128.04154999322077, Width: 10.5, Height: 8
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Text: 'U', X: 94.88125335882626, Y: 141.87286412576685, Width: 10.5, Height: 8
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Text: 'C', X: 91.06561886658267, Y: 158.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 91.06561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 91.06561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 91.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 108.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 126.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 143.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 161.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 178.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 178.56561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 178.56561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 178.56561886658267, Y: 158.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 178.56561886658267, Y: 138.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 178.56561886658267, Y: 118.95182584542655, Width: 10.5, Height: 8
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Text: 'C', X: 178.56561886658267, Y: 98.95182584542655, Width: 10.5, Height: 8
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Text: 'U', X: 178.56561886658267, Y: 78.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 178.56561886658267, Y: 58.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 178.56561886658267, Y: 38.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 179.5058200051398, Y: 21.477077958505106, Width: 10.5, Height: 8
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Text: 'A', X: 194.81561886658267, Y: 13.0, Width: 10.5, Height: 8
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Text: 'U', X: 210.12541772802552, Y: 21.477077958505106, Width: 10.5, Height: 8
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Text: 'C', X: 211.06561886658267, Y: 38.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 211.06561886658267, Y: 58.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 211.06561886658267, Y: 78.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 211.06561886658267, Y: 98.95182584542655, Width: 10.5, Height: 8
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Text: 'U', X: 211.06561886658267, Y: 118.95182584542655, Width: 10.5, Height: 8
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Text: 'A', X: 211.06561886658267, Y: 138.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 211.06561886658267, Y: 158.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 211.06561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 211.06561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 211.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 228.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 246.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 246.06561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 246.06561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 246.06561886658267, Y: 158.95182584542653, Width: 10.5, Height: 8
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Text: 'C', X: 234.41055079229898, Y: 145.89771165724642, Width: 10.5, Height: 8
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Text: 'A', X: 231.72740817603437, Y: 128.60461318545663, Width: 10.5, Height: 8
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Text: 'C', X: 238.87886425987801, Y: 112.63253802488063, Width: 10.5, Height: 8
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Text: 'A', X: 253.56561159438235, Y: 103.11676365877341, Width: 10.5, Height: 8
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Text: 'U', X: 271.065626138783, Y: 103.11676365877341, Width: 10.5, Height: 8
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Text: 'G', X: 285.7523734732873, Y: 112.63253802488063, Width: 10.5, Height: 8
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Text: 'U', X: 292.90382955713096, Y: 128.60461318545663, Width: 10.5, Height: 8
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Text: 'U', X: 290.22068694086636, Y: 145.89771165724642, Width: 10.5, Height: 8
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Text: 'A', X: 278.56561886658267, Y: 158.95182584542653, Width: 10.5, Height: 8
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Text: 'U', X: 278.56561886658267, Y: 178.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 278.56561886658267, Y: 198.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 278.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 296.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 313.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 331.06561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'G', X: 348.56561886658267, Y: 218.95182584542653, Width: 10.5, Height: 8
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Text: 'A', X: 366.06561886658267, Y: 218.95182584542655, Width: 10.5, Height: 8
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Text: 'A', X: 383.56561886658267, Y: 218.95182584542655, Width: 10.5, Height: 8
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Text: 'U', X: 401.06561886658267, Y: 218.95182584542655, Width: 10.5, Height: 8
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Text: 'U', X: 418.56561886658267, Y: 218.95182584542655, Width: 10.5, Height: 8
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Text: 'A', X: 436.06561886658267, Y: 218.95182584542655, Width: 10.5, Height: 8
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Text: 'A', X: 453.56561886658267, Y: 218.95182584542655, Width: 10.5, Height: 8
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Text: '1', X: 9.315618866582668, Y: 238.95182584542653, Width: 9.0, Height: 8
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Text: '10', X: 35.53524985556099, Y: 48.75198767397748, Width: 18.0, Height: 8
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Text: '20', X: 37.31561886658267, Y: 238.95182584542653, Width: 18.0, Height: 8
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Text: '30', X: 83.3792257192556, Y: 80.36309725797133, Width: 18.0, Height: 8
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Text: '40', X: 139.81561886658267, Y: 238.95182584542653, Width: 18.0, Height: 8
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Text: '50', X: 154.81561886658267, Y: 58.95182584542653, Width: 18.0, Height: 8
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Text: '60', X: 227.31561886658267, Y: 138.95182584542653, Width: 18.0, Height: 8
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Text: '70', X: 212.5773228157805, Y: 154.44153199414836, Width: 18.0, Height: 8
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Text: '80', X: 294.81561886658267, Y: 198.95182584542653, Width: 18.0, Height: 8
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Text: '90', X: 432.31561886658267, Y: 238.95182584542655, Width: 18.0, Height: 8
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Text: '91', X: 449.81561886658267, Y: 238.95182584542655, Width: 18.0, Height: 8
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Text: 'SON, -28.9 ± 0.7
 kcal/mol, AUC: 0.915', X: 163.15780943329133, Y: 251.75182584542657, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 467.81561886658267, 251.75182584542657)
Updated viewBox: -0.25 0.0 473.06561886658267 256.75182584542654
Updated SVG: /disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/2e4f7d7c-7b6f-48e5-bfa3-e7db0b2ebd6a/final_image/SON_fold_final_1.svg
